Thank you so much David.

I have re-installed the R and all the packages. It did not solved the problem. What else can I do?

Many thanks

Jing

From: "DavidvonPKU@gmail.com<mailto:DavidvonPKU@gmail.com>" <DavidvonPKU@gmail.com<mailto:DavidvonPKU@gmail.com>>
Date: Tue, 12 Jul 2011 10:54:44 -0700
To: Jing Huang <huangji@ohsu.edu<mailto:huangji@ohsu.edu>>
Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>>
Subject: Re: [BioC] KEGGgraph

Hi dear Jian,

This is due to the old dependency of KEGGgraph on the Rgraphviz package. It is solved in the devel version. Please try to re-install the Rgraphviz package, or update to the devel version of KEGGgraph.

Best wishes,
David

Am schrieb Jing Huang <huangji@ohsu.edu<mailto:huangji@ohsu.edu>>:
> Hi,
>
>
>
> I am trying to run KEGGgraph and run into this problem.  Can somebody help me with this? It happens only if I run the program on IMAC (10.6.8 or 10.6.6)
>
>
>
>
>
> > library(Rgraphviz)
>
> > nodeInfo
> > nodeType
> > makeNodeRenderAttrs
> + shape="ellipse", fill="#e0e0e0",...) {
>
> + rv
> + nA
> + for(i in seq(along=rv)) {
>
> + if (length(rv[[i]]) == 1) {
>
> + rv[[i]]
> + } else {
>
> + if (length(rv[[i]]) != numNodes(g))
>
> + stop("Attribute vector must have as many elements as 'g' has nodes.")
>
> + }
>
> + names(rv[[i]])
> + nA[[ names(rv)[[i]] ]]
> + }
>
> + nodeRenderInfo(g)
> + return(g)
>
> + }
>
> > toyDrawn
>
>
> *** caught segfault ***
>
> address 0x10, cause 'memory not mapped'
>
>
>
> Traceback:
>
>  1: .Call("Rgraphviz_doLayout", graph, as.integer(type), PACKAGE = "Rgraphviz")
>
>  2: graphLayout(g)
>
>  3: agopen(x, name = name, layoutType = layoutType, recipEdges = recipEdges,     nodeAttrs = nodeAttrs, edgeAttrs = edgeAttrs, attrs = attrs,     ...)
>
>  4: layoutFun(x, ...)
>
>  5: layoutGraph(graph)
>
>  6: plotKEGGgraph(toyGraph)
>
>
>
> Possible actions:
>
> 1: abort (with core dump, if enabled)
>
> 2: normal R exit
>
> 3: exit R without saving workspace
>
> 4: exit R saving workspace
>
>
>
> Many Thanks
>
>
>
> Jing Huang
>
>
>
> Oregon Health & Sciences University
>
> Radiation Oncology
>
>
>
>
>
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>
>
>
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>
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>
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>
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